pairwise_termsim
Get the similarity matrix
pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 30) ## S4 method for signature 'enrichResult' pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 200) ## S4 method for signature 'gseaResult' pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 200) ## S4 method for signature 'compareClusterResult' pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 200) pairwise_termsim.enrichResult( x, method = "JC", semData = NULL, showCategory = 200 ) pairwise_termsim.compareClusterResult( x, method = "JC", semData = NULL, showCategory = 200 )
x |
enrichment result. |
method |
method of calculating the similarity between nodes, one of "Resnik", "Lin", "Rel", "Jiang" , "Wang" and "JC"(Jaccard similarity coefficient) methods. |
semData |
GOSemSimDATA object |
showCategory |
number of enriched terms to display |
This function add similarity matrix to the termsim slot of enrichment result.
## Not run: library(clusterProfiler) library(org.Hs.eg.db) library(enrichplot) library(GOSemSim) library(DOSE) data(geneList) gene <- names(geneList)[abs(geneList) > 2] ego <- enrichGO(gene = gene, universe = names(geneList), OrgDb = org.Hs.eg.db, ont = "BP", pAdjustMethod = "BH", pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = TRUE) d <- godata('org.Hs.eg.db', ont="BP") ego2 <- pairwise_termsim(ego, method="Wang", semData = d) emapplot(ego2) emapplot_cluster(ego2) ## End(Not run)
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